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Synj2 synaptojanin 2 [ Rattus norvegicus (Norway rat) ]

Gene ID: 84018, updated on 10-Jul-2024

Summary

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Official Symbol
Synj2provided by RGD
Official Full Name
synaptojanin 2provided by RGD
Primary source
RGD:69436
See related
EnsemblRapid:ENSRNOG00000017114 AllianceGenome:RGD:69436
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Enables phosphatase activity and protein domain specific binding activity. Involved in brain development; dephosphorylation; and intracellular distribution of mitochondria. Located in several cellular components, including cytoplasmic microtubule; perinuclear region of cytoplasm; and ruffle membrane. Is extrinsic component of mitochondrial outer membrane. Is active in presynapse. Orthologous to human SYNJ2 (synaptojanin 2). [provided by Alliance of Genome Resources, Apr 2022]
Annotation information
Annotation category: suggests misassembly
Expression
Biased expression in Heart (RPKM 117.1), Lung (RPKM 78.4) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Synj2 in Genome Data Viewer
Location:
1q11
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (48923742..49027153)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (46518594..46621919)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (46835922..46932544)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134484994 Neighboring gene sorting nexin 9 Neighboring gene mRNA turnover 4, ribosome maturation factor, pseudogene 2 Neighboring gene uncharacterized LOC134482645 Neighboring gene uncharacterized LOC134482650 Neighboring gene uncharacterized LOC120099116 Neighboring gene serine active site containing 1 Neighboring gene general transcription factor IIH subunit 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Localization of mRNAs for synaptojanin isoforms in the brain of developing and mature rats. Kudo M, et al. Brain Res Mol Brain Res, 1999 Feb 5. PMID 9931483
  2. Developmentally regulated alternative splicing in a novel synaptojanin. Khvotchev M, et al. J Biol Chem, 1998 Jan 23. PMID 9442075
  3. Synaptojanin 2, a novel synaptojanin isoform with a distinct targeting domain and expression pattern. Nemoto Y, et al. J Biol Chem, 1997 Dec 5. PMID 9388224
  4. Recruitment of an alternatively spliced form of synaptojanin 2 to mitochondria by the interaction with the PDZ domain of a mitochondrial outer membrane protein. Nemoto Y, et al. EMBO J, 1999 Jun 1. PMID 10357812, Free PMC Article
  5. Identification and characterization of a synaptojanin 2 splice isoform predominantly expressed in nerve terminals. Nemoto Y, et al. J Biol Chem, 2001 Nov 2. PMID 11498538

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
NOT enables PDZ domain binding IBA
Inferred from Biological aspect of Ancestor
more info
  
NOT enables PDZ domain binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables PDZ domain binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables SH3 domain binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables SH3 domain binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables inositol phosphate phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables inositol-1,4,5-trisphosphate 5-phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol monophosphate phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ISO
Inferred from Sequence Orthology
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in inositol phosphate catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in phosphatidylinositol dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phosphatidylinositol dephosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in phosphatidylinositol dephosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synaptic vesicle endocytosis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in axon terminus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic microtubule IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane raft IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
is_active_in perinuclear region of cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in presynapse IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in presynapse IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ruffle membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
synaptojanin-2
Names
synaptic inositol 1,4,5-trisphosphate 5-phosphatase 2
NP_001106842.1
NP_001106843.1
NP_114460.2
XP_038948605.1
XP_038948607.1
XP_038948608.1
XP_038948612.1
XP_038948615.1
XP_063131749.1
XP_063131753.1
XP_063131756.1
XP_063131758.1
XP_063131769.1
XP_063131777.1
XP_063131784.1
XP_063131788.1
XP_063131789.1
XP_063131792.1
XP_063131795.1
XP_063131798.1
XP_063131802.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001113371.1 → NP_001106842.1  synaptojanin-2 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AY034051, BI290811, CK653289, U90312
    UniProtKB/Swiss-Prot
    O55207, Q91ZD8, Q91ZD9
    UniProtKB/TrEMBL
    A6KNZ4
    Related
    ENSRNOP00000104494.1, ENSRNOT00000149366.1
    Conserved Domains (3) summary
    pfam02383
    Location:61 → 342
    Syja_N; SacI homology domain
    pfam08952
    Location:889 → 1025
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:547 → 878
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

  2. NM_001113372.1 → NP_001106843.1  synaptojanin-2 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an internal coding exon, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
    Source sequence(s)
    AY034050, BI290811, CK653289, U90312
    UniProtKB/TrEMBL
    A6KNZ5
    Conserved Domains (3) summary
    pfam02383
    Location:61 → 342
    Syja_N; SacI homology domain
    pfam08952
    Location:889 → 1025
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:547 → 878
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

  3. NM_032071.3 → NP_114460.2  synaptojanin-2 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an internal coding exon and has an additional exon in the 3' region, as compared to variant 1. The resulting isoform (3) lacks an internal segment and has a shorter and distinct C-terminus, as compared to isoform 1.
    Source sequence(s)
    JAXUCZ010000001
    UniProtKB/TrEMBL
    A6KNZ5, A6KNZ7, F1M2D6
    Related
    ENSRNOP00000063385.4, ENSRNOT00000068476.6
    Conserved Domains (3) summary
    COG5329
    Location:28 → 485
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam08952
    Location:889 → 1025
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:547 → 878
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    48923742..49027153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063275683.1 → XP_063131753.1  synaptojanin-2 isoform X3

    UniProtKB/TrEMBL
    A6KNZ4

  2. XM_039092679.2 → XP_038948607.1  synaptojanin-2 isoform X6

    UniProtKB/TrEMBL
    A6KNZ5
    Conserved Domains (3) summary
    COG5329
    Location:28 → 485
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam08952
    Location:889 → 1025
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:547 → 878
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

  3. XM_063275688.1 → XP_063131758.1  synaptojanin-2 isoform X5

    UniProtKB/TrEMBL
    A6KNZ4

  4. XM_063275686.1 → XP_063131756.1  synaptojanin-2 isoform X4

    UniProtKB/TrEMBL
    A6KNZ8, F1M0S5
    Related
    ENSRNOP00000059744.4, ENSRNOT00000066798.6

  5. XM_039092680.2 → XP_038948608.1  synaptojanin-2 isoform X7

    UniProtKB/TrEMBL
    A6KNZ5
    Conserved Domains (3) summary
    COG5329
    Location:28 → 485
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam08952
    Location:872 → 1008
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:530 → 861
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

  6. XM_063275679.1 → XP_063131749.1  synaptojanin-2 isoform X1

    UniProtKB/TrEMBL
    A6KNZ4, A6KNZ6
    Related
    ENSRNOP00000112432.1, ENSRNOT00000129353.1

  7. XM_039092677.2 → XP_038948605.1  synaptojanin-2 isoform X2

    UniProtKB/TrEMBL
    A6KNZ5
    Conserved Domains (4) summary
    COG5329
    Location:28 → 485
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam08952
    Location:872 → 1008
    DUF1866; Domain of unknown function (DUF1866)
    pfam16014
    Location:1243 → 1288
    SAP130_C; Histone deacetylase complex subunit SAP130 C-terminus
    cl00490
    Location:530 → 861
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

  8. XM_063275732.1 → XP_063131802.1  synaptojanin-2 isoform X18

    UniProtKB/TrEMBL
    A6KNZ4

  9. XM_039092684.2 → XP_038948612.1  synaptojanin-2 isoform X8

    UniProtKB/TrEMBL
    A6KNZ5
    Conserved Domains (3) summary
    COG5329
    Location:28 → 485
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam08952
    Location:872 → 1008
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:530 → 861
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

  10. XM_063275725.1 → XP_063131795.1  synaptojanin-2 isoform X16

    UniProtKB/TrEMBL
    A6KNZ8

  11. XM_063275722.1 → XP_063131792.1  synaptojanin-2 isoform X15

    UniProtKB/TrEMBL
    A6KNZ8

  12. XM_063275719.1 → XP_063131789.1  synaptojanin-2 isoform X14

    UniProtKB/TrEMBL
    A6KNZ8

  13. XM_063275699.1 → XP_063131769.1  synaptojanin-2 isoform X9

    UniProtKB/TrEMBL
    A6KNZ9

  14. XM_039092687.2 → XP_038948615.1  synaptojanin-2 isoform X11

    UniProtKB/TrEMBL
    A6KNZ9
    Conserved Domains (4) summary
    COG5329
    Location:13 → 169
    COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
    pfam08952
    Location:573 → 709
    DUF1866; Domain of unknown function (DUF1866)
    pfam16014
    Location:944 → 989
    SAP130_C; Histone deacetylase complex subunit SAP130 C-terminus
    cl00490
    Location:231 → 562
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

  15. XM_063275707.1 → XP_063131777.1  synaptojanin-2 isoform X10

    UniProtKB/TrEMBL
    A6KNZ9

  16. XM_063275718.1 → XP_063131788.1  synaptojanin-2 isoform X13

    UniProtKB/TrEMBL
    A6KNZ9, F1LPP1
    Related
    ENSRNOP00000062564.4, ENSRNOT00000067661.5

  17. XM_063275728.1 → XP_063131798.1  synaptojanin-2 isoform X17

    UniProtKB/TrEMBL
    A6KNZ8

  18. XM_063275714.1 → XP_063131784.1  synaptojanin-2 isoform X12

    UniProtKB/TrEMBL
    A6KNZ9
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O55207.2 GenPept UniProtKB/Swiss-Prot:O55207

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